Q GO:0071051 polyadenylation-dependent snoRNA 3'-end processing under

[ValWood]

I was going to move

GO:0071051 polyadenylation-dependent snoRNA 3'-end processing under

co-transcriptional RNA 3'-end processing, cleavage and polyadenylation pathway Any process involved in transcription termination-coupled 3’ processing of RNA polymerase II RNA transcripts by the 3′ end cleavage and addition of the poly(A) tail.\nThis pathway is required for the maturation of primary protein-encoding transcripts into functional RNAs that can be exported from the nucleus and translated in the cytoplasm, but is also required for polyadenylation-dependent decay."

but because it is defined: Any process involved in forming the mature 3' end of a snoRNA molecule linked to prior polyadenylation of the 3'-end of the precursor snoRNA.

I'm not completely sure which process this term is referring to. I thought that the polyadenylation was part of the end processing pathway?

@krchristie would this move make sense? Is this what the term was intended for?

[ValWood]

The annotations are to exosome, and TRAMP. TRAMP has polyadenylation activity.

non-canonical polymerases uses a different regulated sequence in the RNA and specifies RNAs for degeneration or processing.[13]

but it can't go under this term because it isn't co-trancriptional.

https://www.dovepress.com/current-perspectives-on-the-role-of-tramp-in-nuclear-rna-surveillance--peer-reviewed-fulltext-article-RRBC

The main function of TRAMP is to assist the nuclear exosome to degrade a large variety of RNA substrates, such as hypomodified initiator tRNAiMet, abnormally processed ribonucleic RNAs (rRNAs),4–6 cryptic unstable transcripts (CUTs),7–10 long noncoding RNAs (lncRNAs),11 microRNAs (miRNAs),12,13 and normal by-products of RNA metabolism such as spliced-out introns,14,15 and to be involved in the many other RNA processes such as the maturation steps in precursor RNA processing and transfer RNA (tRNA) editing.16

Therefore, it is not surprising that the TRAMP complex is also directly involved in many RNA processing pathways such as splicing,15,17,18 RNA export,19,20 and heterochromatic gene silencing,21,22

[ValWood]

I'll leave this term for now and come back to it.

[ValWood]

Actually my suggestion is to merge this term into

GO:0071036 nuclear polyadenylation-dependent snoRNA catabolic process The chemical reactions and pathways occurring in the nucleus and resulting in the breakdown of a small nucleolar RNA (snoRNA) molecule, initiated by the enzymatic addition of a sequence of adenylyl residues (polyadenylation) at the 3' end the target snoRNA. PMID:15935758

since it is referring to the same pathway.

snos polyadenylated by TRAMP are destined for degradation. The term GO:0071051 polyadenylation-dependent snoRNA 3'-end processing is confusing because it's an additional way to describe steps in the same pathway.

All of the other end-processing terms refer to maturation, but this particular term is an odd man out because its part of a degradation pathway.

[ValWood]

Paper summary These data strongly suggest that polyadenylation by Pap1 and Trf4 polymerases linked to transcription termination is an intrinsic step in the snoRNA pathway that stimulates 3′ end formation by the exosome.

During the final steps of maturation, snoRNA fate is decided, and incorrectly processed or misassembled molecules are degraded by TRAMP and the exosome.

This paper looks as though it is assaying both the end-processing for maturation and the polyadenylation events surrounding the processing of misassembly molecules via TRAMP.

The annotations here are to the TRAMP pathway and exosome, this is the route for incorrectly processed or missassembly molecules (i.e they feed directly into the decay pathway).

They imply this pathway is also processing the snoRNAs, but I'm not sure how maturation of functional and non-functional molecules can be distinguished, so I'd like to check some later papers on this pathway.

[ValWood]

Closing, I will open a new ticket for snoRNA processing.

This term is mentioned in other tickets and it's quite confusing because all of the pathways are polyadenylation -dependent, some mRNA cleavage and polyadenylation factor dependent, and some, some TRAMP/exosome:

i.e.

[ValWood]

changed closed status

[ValWood]

f